﻿The title of this blog is dedicated to those world views which mistake necessary for sufficient
conditions, view reasoning as reducible to physics, and substitute reality with imagination. A subtitle of
this blog could be “Reality Deficit,” since it endeavours to deal with world views, statements and
definitions of existence which are inconsistent or deficient in reality. Invest or spend this reality
cheque as you see fit, and please don’t hesitate to inform me if it ever bounces.

Welcome

I attack worldviews that are inconsistent. I do not attack people. Please contribute. I welcome constructive and negative criticism, however personal attacks and character assassinations do not a logical argument make.

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Galileo Galilei

I do not feel obliged to believe that the same god who has endowed us with sense, reason and intellect has intended us to forgo their use.

Albert Einstein

The scientist's religious feeling takes the form of
rapturous amazement at the harmony of natural law, which reveals an intelligence of such superiority that, compared with it, all the systematic thinking and acting of human beings is an utterly insignificant reflection.
(The World As I See It, p.9)

Robert Wright

Its amazing that a process as amoral and crassly pragmatic as natural selection could design [!] a mental organ that makes us feel as if we’re in touch with higher truths. Truly a shameless ploy.

Sir Francis Bacon, "Novum Organum"

“Lastly, there are others who appear anxious lest there should be something discovered in the investigation of nature to overthrow, or at least shake religion, particularly among the unlearned. The two last apprehensions appear to resemble animal instinct, as if men were diffident, in the bottom of their minds, and secret meditations, of the strength of religion, and the empire of faith over the senses; and therefore feared that some danger awaited them from an inquiry into nature. But any one who properly considers the subject, will find natural philosophy to be, after the word of God, the surest remedy against superstition, and the most approved support of faith. She [i.e., natural philosophy=science] is therefore rightly bestowed upon religion as a most faithful attendant, for the one exhibits the will and the other the power of God.”

J. B. S. Haldane

But if death will probably be the end of me as a finite individual mind, that does not mean that it will be the end of me altogether. It seems to me immensely unlikely that mind is a mere by-product of matter.
For if my mental processes are determined wholly by the motions of atoms in my brain I have a no reason to suppose that my beliefs are true. They may be sound chemically, but that does
not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.
In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter. But as regards my own very finite and imperfect mind, I can see, by studying the effects on it of drugs, alcohol, disease, and so on, that. its limitations are largely at least due to my body.”
“When I Am Dead”, Possible Worlds: And Other Essays

Max Planck

﻿“All matter originates and exists only by virtue of a force which brings the particles of an atom to vibration and holds this minute solar system of the atom together . . . . We must assume behind this force the existence of a conscious and intelligent mind.”
(during his Nobel acceptance speech)

Louis Pasteur

The more I study nature, the more I stand amazed at the work of the Creator.
“Louis Pasteur—Founder of Modern Medicine”

C. S. Lewis

﻿If the solar system was brought about by an accidental collision, then the appearance of organic life on this planet was also an accident, and the whole evolution of Man was an accident too. If so, then all our present thoughts are mere accidents - the accidental by-product of the movement of atoms. And this holds for the thoughts of the materialists and astronomers as well as for anyone else's. But if their thoughts - i.e., of Materialism and Astronomy - are merely accidental by-products, why should we believe them to be true? I see no reason for believing that one accident should be
able to give me a correct account of all the other accidents. It's like expecting that the accidental
shape taken by the splash when you upset a milk-jug should give you a correct account of how the jug was made and why it was upset.

Cyril Burt (British neurologist)

﻿A comparison of the specific micro-neural situations in which consciousness does and does not arise suggests that the brain functions not as a generator of consciousness, but rather as a two-way transmitter and detector, i.e., although its activity is apparently a necessary condition, it cannot be a sufficient condition of conscious experience.

G. K. Chesterton

﻿. . . The Darwinians have this mark of fighters for a lost cause, that they are perpetually appealing to sentiment and to authority. Put your bat or your rhinoceros simply and innocently as a child might put them, before the Darwinian, and he will answer by an appeal to authority. He will probably answer with the names of various German professors; he will not answer with any ordinary English words, explaining the point at issue. God condescended to argue with Job, but the last Darwinian will not condescend to argue with you. He will inform you of your ignorance; he will not enlighten your ignorance.
And I will add this point of merely personal experience of humanity: when men have a real explanation they explain it, eagerly and copiously and in common speech, as Huxley freely gave it when he thought he had it. When they have no explanation to offer, they give short dignified replies, disdainful of the ignorance of the multitude.
(published in 1920)

Robert Jastrow

﻿A sound explanation may exist for the explosive birth of our Universe; but if it does, science cannot find out what the explanation is. The scientist’s pursuit of the past ends in the moment of creation. This is an exceedingly strange development, unexpected by all but the theologians. They have always accepted the word of the Bible: In the beginning God created heaven and earth… At this moment it seems as though science will never be able to raise the curtain on the mystery of creation. For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.

Saturday, February 23, 2008

Published Method of Measuring Specificity (Function)

It looks like a PNAS article has finally caught up with and refined some of the work of Dr. Dembski. Here is the PNAS article that discusses measuring for functional information, and upon first read through seems to measure functional information in an extremely similar manner as Dr. Dembski measures for specificity as it relates to function in "Specification: the Pattern that Signifies Intelligence."

It seems that the main and only significant difference is that the PNAS article uses a measure of functionality (specificity) that doesn't rely on a human linguistic description of the pattern. Although the equation seems to be the same as far as I can tell (log2 [number of specified patterns related to the function * probability of the pattern in question]), the gauge for the number of specified patterns seems to be taken directly from the "independent" description as formulated by the system in question -- ie: the relation between biological function and its independent description in a specified RNA chain as opposed to an independent linguistic description of the biological function. IMO, this provides a more concrete and accurate measure of specificity and still does not detract from Dembski's work on CSI in any way as I had already basically incorporated that same method as used in the recently published paper when I discussed specifications here on this blog. As I have explained: "Now, let’s take a look at proteins. When it comes to measuring specificity, this is exactly like measuring specificity in a meaningful sentence, as I will soon show. Functional specificity merely separates functional pattern “islands” from the sea of random possible patterns. When specific proteins are brought together, you can have a pattern which creates function. That functional pattern itself is formulated by information contained in DNA which is encoded into RNA and decoded into the specific system of functional proteins. The functional pattern as the event in question is defined independently as a pattern of nucleic acids ... When measuring for a functional specification (within a set of functional "islands"), you apply the same equation, however, when measuring the specificity you take into account all other FUNCTIONAL patterns (able to be processed into function *by the system in question*) that have the same probability of appearance as the pattern in question."

As far as I can tell, the PNAS paper doesn't take into account any probabilistic resources, so it is not measuring for CSI; it only measures for SI, that is, specified or functional information (presented as a measure of complexity).

From the PNAS article:"Functional information provides a measure of complexity by quantifying the probability that an arbitrary configuration of a system of numerous interacting agents (and hence a combinatorially large number of different configurations) will achieve a specified degree of function."

...and...

"Letter sequences, Avida genomes and biopolymers all display degrees of functions that are not attainable with individual agents (a single letter, machine instruction, or RNA nucleotide, respectively). In all three cases, highly functional configurations comprise only a small fraction of all possible sequences."

Of course, Dembski's definition of specificity does take specificity beyond merely function, however, in his discussion specificity most definitely includes function and the measurement seems to be in agreement with this recent PNAS article. According to Dembski's definition, specificity includes algorithmic compressibility, semantic meaning, and function. However, the other article uses specificity in a more strict functional sense which includes meaning and other "usable" function, and unlike Dembski has done, this PNAS article doesn't seem to even really attempt to provide a rigorous definition of a specified pattern. Dr. Dembski has defined a specified pattern as an event which can be formulated as a conditionally independent pattern. Of course, as I've already explained and shown, this includes algorithmically compressible patterns, as well as semantically meaningful events and functional events.

Compare the above PNAS article with Dembski's treatment of specificity and check it out for yourself.

No comments:

﻿If the whole universe has no meaning, we should never have found out that it has no meaning: just
as, if there were no light in the universe and therefore no creatures with eyes, we should never know
it was dark. Dark would be without meaning.

Albert Einstein

﻿The most incomprehensible thing about the universe is that it is comprehensible.

About Me

I am a Christian and I believe that the universe and life was designed on purpose, with a purpose, and for a purpose. I believe that objective truth and reality do exist and can be discovered through reasoning. Regarding evolution, natural selection and evolution obviously occur, however the use of natural selection to produce increase of complex and specified information is not possible absent the existence of previous highly improbable and specified information not defined by physical properties of material used. I could be seen as a theistic evolutionist who also believes that the foundational tenets of Intelligent Design Theory are both scientific and correct.
I describe myself as a realist and I also enjoy cooking and snowboarding.